Download all variants

You can download a VCF file that contains all variants that are included in an analysis, and other files that contain information for the variants. You can also download a batch of filtered variant files from multiple analyses simultaneously.
  1. In the Analyses tab, click Overview, then select the analysis of interest.
  2. Use one of the following options to download a compressed directory of files that contains data for all variants in the analysis:
    To . . . Do this . . .
    Download a set of files that contain data for variants that are filtered from a single analysis.

    • Select the row for the analysis of interest, then click Actions > Download All Variants.

    • Click the hyperlink for the name of the Analysis to open the Analysis Results screen, then click Download > All Variants.

    • Click the hyperlink for the name of the Analysis to open the Analysis Results screen, then click Visualize, In the Analysis Visualization click Download > All Variants.

    Note: The set of downloaded filtered variants files are identical for all of these options.
    Download a set of files that contain data for variants that are filtered from multiple analyses. Select rows for multiple analyses of interest, then click Actions > Export next to Selected Analyses.

    A compressed directory that is named analysis name_All.zip is downloaded.

  3. To download the ZIP file from Ion Reporter™ Software:
    1. Open the Home tab, then click Notifications.
    2. Find the download file in the list. You can click Downloads to narrow the list, or see the timestamp.
    3. Click (Download).
  4. Extract the contents of the directory to access the folders and files.

    Folder

    Description of contents

    CNV_VCIB

    • cn_results.png, a file that represents the CNV amplicons in the X scale and log2 ratio in Y scale. Open the file with a text editor.

    • amplicon_data.txt

    CnvActor

    Gene_deletions.xls, a file that contains information about whole gene deletions and amplicon coverage that are found in BRCA analyses. Values in the third column of the file indicate the following information for the BRCA1 and BRCA2 genes in the sample.

    • S—Stable.
    • SQCFAIL—Calculated overall variation between amplicon coverage is too high.
    • LGD=<score>—Large Gene Deletion with Phred scale score = <score>.
    • WGD=<score>—Whole Gene Deletion with Phred scale score = <score> (max score = 100).

    The Phred scale score must be >=40, for the WGD (subtype = GeneCNV) to be reported in the VCF file. Large gene deletions are not reported in the VCF file.

    QC

    • report.pdf

    • Torrent Suite™ Software Quality Control (QC files. For example, bam_file_basename>.ionstats_alignment.json, analysis.bfmask.stats, explog_final.txt, raw_peak_signal, InitLog.txt, basecaller_results/BaseCaller.json, basecaller_results/ datasets_basecaller.json, basecaller_results/ionstats_tf.json, basecaller_results/TFStats.json

    • mapd.txt

    • diffCoverage.seg

    • RNAQCAndCalls.txt

    • TotalMappedFusionPanelReads.txt

    • qc_cnv_display.txt

    • <analysis name>_QC.pdf

    StatsActor

      • amplicons_low_no_coverage_statistics.txt

      • analysis_low_no_coverage_statistics.txt

      • genes_low_no_coverage_statistics.txt

    • AnnotatorActor

      • variome-stats.csv

    Variants

    Contains VCF and TSV files for the CNV variants. You can open these files in Microsoft™ Excel™.

    Note: If the Ion Reporter™ Software analysis includes notes, the notes are included in the files in a row named #analysisnotes.

    • <analysis name><timestamp>.oncomine.tsv

    • <analysis name><timestamp>.vcf

    • <analysis name><timestamp>.full.tsv

    • SmallVariants.filtered.vcf

    • SmallVariants.vcf

    • Variant.filtered.genome.vcf

    Workflow_Settings

    • Analysis_Settings —Contains a text file that describes settings used for the analysis. Open the file with a text editor.

    • Module_Configuration_Files—Contains configuration files for workflows, including VariantCallerActor.json, a JSON file that contains variant finding parameters used to customize variant calling in Ion Reporter™ Software and the settings used in the analysis. The file shows changes made to the parameters in the software. The file is present only for analyses that contain variants.

    fusions_RNAExonVariants_normCounts.png

    HRR_Results

    Contains a .TSV file that contains a summary of the HRR results.

    signature_prediction

    The signature_prediction folder contains:

    • A PDF report of the mutational signature prediction results

    • Image files that graphically represent the results (Only available if a mutational signature match is found.)

    • A TXT file of the trinucleotide distribution of Variants

    MSI

    Files with data about microsatellite instability (MSI) markers. These markers can identify a form of genomic instability in the replication of repetitive DNA. MSI often occurs in tumor cells. It leads to the appearance of multiple alleles at microsatellite loci, which can be easily identified.

    • Summary.tsv—Provides a summary of results for MSI markers, as shown in the Analysis Results table, and additional information about the algorithm version that is used to calculate the Marker MSI Score and MSI Score.

    • Details.tsv—Provides marker-level information on microsatellite instability, such as individual marker MSI scores, and read coverage for individual MSI markers.

    • MSIQC.json —File contains "flags" and warning messages associated with MSI status that are used by customer support representatives.

    RESULTS

    If the Tumor Mutational Burden parameter is enabled, or an analysis workflow for the Tumor Mutation Load Assay is used, a Results folder is generated that contains:

    • filter_variants.tsv and somatic_variants.tsv—TSV files that contain post-filter and somatic variants.

    • <tmb report>.pdf—PDF report that contains tumor mutational load results.

    • statistic.txt—contains tumor mutational burden statistics.

    • PNG files that contain images of:

      • allele frequency distribution of germline and somatic variants

      • allele frequency distribution of only somatic variants

      • bar plot of signature type and context of somatic mutations

      • pie chart of substitution type of somatic mutations

      • pie chart of signature pattern of somatic mutations

    • base_change_file.txt and somatic_mutation_substitution_context_summary.txt— files that contain the data used to generate the substitution type and context of somatic mutations and substitution type and signature pattern of somatic mutations plots

    • deamination_metric.txt — contains the TMB score and other TMB metrics

    Plugin outputs

    Contains ZIP file of the plugin output directory.

    Immune repertoire output

    The CSV, PNG and PDF files that show the data for immune repertoire analyses.

    • <analysis name><timestamp>.csv

    • <analysis name><timestamp>.png

    • <analysis name><timestamp>.pdf

    Metagenomics Output

    Files from a single metagenomics sample, or results from multiple samples that the software compares for Beta diversity, and files that contains reads for the analysis in FASTA format, and other TXT files for the analysis.

    To download all results files for metagenomics analyses, use instead the Download results files for all samples link, shown in the Visualization/Downloads section of the metagenomics analysis results. For more information, see View interactive taxonomy charts for metagenomics analyses.

You can view the extracted files individually, or upload a VCF file to a software application that requires VCF files, such as Oncomine™ Reporter Software.

Related Topics
Parent topic: Variants file downloads